Thomas is only 15 seconds off Sagan's lead, while Nibali, Dumoulin and Uran are among a big group of riders at 16 seconds.

"We have one of the strongest teams here so hopefully we can take back some time," Porte said.

BMC reported in their media release soon after stage two that Porte had not lost any more time.

But nearly four hours after the end of the 182.5km sprint stage from Mouilleron-Saint Germain to La Roche-Sur-Yon, race organisers made sweeping changes to the results.

Race judges apparently made an initial error with the times after crashes and mechanical problems marred the last few kilometres of stage two.

The changes meant a nasty surprise late in the day for Porte, who is now 71st on the overall standings.

Porte had a flat tyre in the first half of stage two but his teammates ensured he returned to the peloton quickly and he finished the stage out of trouble in 18th position.

Sagan was ahead of the pile-up less than 2km from the finish that took out several riders, including Australian Michael Matthews (Team Sunweb) and Italian stage one winner Fernando Gaviria (Quick-Step).

The Bora-Hansgrohe star held off a fast-finishing Italian Sonny Colbrelli (Bahrain-Merida), while French rider Arnaud Demare (Groupama-FdJ) was third.

The Slovakian was thrown out after the fourth stage 12 months ago for sending Mark Cavendish crashing in a chaotic sprint.

"It's a perfect day, I was a bit scared because Sonny was coming back strong," Sagan said.

"It's a very good start. I'm really back."

The Australian Mitchelton-Scott team had a bad stage, with their overall contender Adam Yates crashing for the second time in two days.

The British star went down with 30km left and Australian teammate Luke Durbridge also had a tumble.